Arsenic and Odd Life

by Paul Gilster on December 2, 2010

As if it were news, one thing the great flap over astrobiology and yesterday afternoon’s NASA news conference tells us is that anything smacking of extraterrestrial life brings over the top commentary long before the findings are officially discussed, as should be clear from some of the Internet blogging about the GFAJ-1 bacterium found in Mono Lake. And what a shame. Despite the astrobiology teaser, GFAJ-1 does not in itself tell us anything about alien life and does not necessarily represent a ‘shadow biosphere,’ a second startup of life on Earth that indicates life launches in any available niche. But the find is remarkable in its own right.

Let’s leave the astrobiology aside for the moment and simply focus on the fact that life is fantastically adaptable in terms of biochemistry, and can pull off surprises at every turn. That’s always a result worth trumpeting, even if it leaves the wilder press speculations in the dust. After all, it’s long been assumed that the six elements that underlay the basic chemistry of life are carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. Despite persistent speculation, few thought life could exist without them.

Now we learn that the GFAJ-1 bacterium found in eastern California’s Mono Lake can, at least in the conditions of a fascinating experiment, use arsenic in its metabolism rather than being poisoned by it. Arsenic occurs in the lake in one of the highest concentrations of any site in the world. Let me quote the ever reliable Caleb Scharf (Columbia University) on arsenic and its role:

Arsenic is an insidious element. With 5 outer valence electrons the arsenic atom is chemically similar to the biologically critical element phosphorus, but only in crude terms. Life depends extensively on phosphorus – it helps form the molecular backbone of DNA, it is part of molecules like Adenosine triphosphate (ATP) that serves as a vital rechargeable chemical battery within all living cells, as well as many other biologically vital roles. Arsenic on the other hand can weasel its way in, waving its valence electrons in a come-hither fashion, and getting the best seat in the house. The problem is that once an organism takes in arsenic, replacing some of its phosphorus, it typically begins to malfunction – arsenic is is a fatter atom and biochemistry is a sensitive thing. There is good reason why arsenic has long been a poison of choice for nefarious human dealings.

Indeed. GFAJ-1 is intriguing because rather than just being tolerant of a toxin like arsenic, it’s actually able to use it. The team working under Felisa Wolfe-Simon (USGS) reported online today in Science that phosphorus is here replaced by arsenic, a case of an alternate building block for life of the kind long speculated about by science fiction writers. This from Nature:

Arsenic is positioned just below phosphorus in the periodic table, and the two elements can play a similar role in chemical reactions. For example, the arsenate ion, AsO43-, has the same tetrahedral structure and bonding sites as phosphate. It is so similar that it can get inside cells by hijacking phosphate’s transport mechanism, contributing to arsenic’s high toxicity to most organisms.

The team proceeded by collecting mud from the lake and adding samples to a salt medium that was high in arsenate, then diluting the material to wash out remaining phosphate. Steeping the cells in arsenic, the scientists discovered an organism that seemed to grow well under these conditions, even after multiple generations since their first collection more than a year ago. What phosphorus was available to the bacteria was present only in traces from the original colony of cells, and in impurities found in the growth medium. Again from Nature:

When the researchers added radio-labelled arsenate to the solution to track its distribution, they found that arsenic was present in the cellular fractions containing the bacterium’s proteins, lipids and metabolites such as ATP and glucose, as well as in the nucleic acids that made up its DNA and RNA. The amounts of arsenate detected were similar to those expected of phosphate in normal cell biochemistry, suggesting that the compound was being used in the same way by the cell.

Can these bacteria replace phosphate with arsenic naturally? Wolfe-Simon herself says thirty years of work remain to figure out exactly what’s going on, a comment on the preliminary nature of this work, which remains controversial in some quarters and is in obvious need of extensive follow-up. No shadow biosphere yet, but obviously the quest is ongoing because of its implications, and we’ve now received one very tantalizing piece of evidence that such things may be possible.

If life really did start here more than once — a finding that is not remotely demonstrated by this work — then we can talk about how likely it will have done the same thing on distant planets, upping the chances that we live in a universe where life emerges whenever given the chance. But we’re hardly there yet, as became evident in the exchanges between Wolfe-Simon and Steven Benner (Foundation for Applied Molecular Evolution) at the news conference. British science writer Ed Yong fleshes out some of the reasons for skepticism:

It’s an amazing result, but even here, there is room for doubt. As mentioned, Wolfe-Simon still found a smidgen of phosphorus in the bacteria by the end of the experiment. The levels were so low that the bacteria shouldn’t have been able to grow but it’s still not clear how important this phosphorus fraction is. Would the bacteria have genuinely been able to survive if there was no phosphorus at all?

Nor is it clear if the arsenic-based molecules are part of the bacteria’s natural portfolio. Bear in mind that Wolfe-Simon cultured these extreme microbes using ever-increasing levels of arsenic. In doing so, she might have artificially selected for bacteria that can use arsenic in place of phosphorus, causing the denizens of Mono Lake to evolve new abilities (or overplay existing ones) under the extreme conditions of the experiment.

And I should also return to Caleb Scharf, who notes that while phosphorus is relatively rare — in terms of cosmic abundance — compared to other major bio-chemically important elements, it is a thousand times more abundant than arsenic, which is little more than a trace by comparison. So much for the idea of entire biospheres crowded with life forms drawing on the stuff, at least in terms of the odds. The GFAJ-1 experiments make for a fascinating story, one that was upstaged by a media circus but remains notable news for all that. Paul Davies, one of the authors of the paper, calls this work ‘the beginning of what promises to be a whole new field of microbiology.’

But again, note the caveat, as Davies explains:

“This organism has dual capability. It can grow with either phosphorous or arsenic. That makes it very peculiar, though it falls short of being some form of truly ‘alien’ life belonging to a different tree of life with a separate origin. However, GFAJ-1 may be a pointer to even weirder organisms. The holy grail would be a microbe that contained no phosphorus at all.”

The paper is Wolfe-Simon et al., “A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus,” published online by Science (2 December 2010). This article in Astrobiology Magazine provides an excellent backgrounder on the Wolfe-Simon team’s methods. Wolfe-Simon’s own Web site is impressive and well worth checking re her ongoing work.

Zen, my impression is identical. They never ran autorads or CsCl gradients of DNA or RNA from certifiably living cells. Having dead/dying/n0n-dividing cells in a bacterial prep is normally not a problem, though it influences the efficiency of whatever you’re trying to produce (plasmid DNA, induced protein, etc). Here it is THE crux of the matter for reasons that we have discussed and more. Frankly, having this paper is Science is a slap in the face of scientists who do their work rigorously and go about in a cold sweat over a single error bar that’s too high.

@ProtoAvatar
While it is true that the biosphere is all one tree of life, this does not mean that biogenesis is constrained to narrow conditions. First of all, life began early in the earths history – just after the hadean period, and possibly during the latter phases. It has not been determined how and where biogenesis took place. There are a variety of possibilities – but a biogenesis deep in the crust or similar “extreme” environment from our view would mean that biogenesis could happen much more frequently. My reasoning is that conditions in the crust or the bottom of the ocean are relatively stable – they are not vulnerable to radiation, impact events, or other causes of extinction. In addition, there are many exoplanets, and it can be safely assumed that “deep, dark” conditions are more common than summer beach habitats.

While there are different possible settings for biogenesis, it may very well be that only one of these scenarios makes it possible. However, even if a hydrothermal vent origin (for example) was proved, that would not preclude other possible biogenesis events in other conditions. Once life spreads and fills niches, a shadow biosphere would be facing stiff competition.

I don’t claim to have all the answers. I’m simply extrapolating from what is currently understood.

[blockquote]But I think we do know, at least to a first approximation — hard radiation and those temperatures simply do not support the long term formation of complex molecules, certainly not the molecules all organisms on earth use in their biological processes.[/blockquote]
True. However, organisms underground/underwater could be safe from radioactive surface conditions, and later evolution could possibly adapt to solar flares and the like.

[blockquote]Sure, but those are all locations that are, as I put it, wet and warm, despite their specific differences, they all have accessible roughly the same chemical and energy environment. Some particular aspects of those environments might be particularly conducive to abiogenesis (such as spaces to isolate chemical reactions), but they aren’t radically different in basic terms.[/blockquote]

A salient point. But as per my previous comment, such conditions are more stable and probably more common.

[blockquote]Sure, it may be that there are various environments that can produce life (although I think ProtoAvatar’s comments are important to consider). That, however, doesn’t mean that we can extrapolate from the environments of extremophiles to what those “genesis” conditions might be. Knowing humans live in Antarctica or in space tells you nothing about the environment in which we originally developed, and having an organism that (may) be adapted to using arsenic doesn’t say anything about the potential role for arsenic in abiogenesis.[/blockquote]

Those two examples are true. Certainly there is a difference between biogenesis and the niches life can fill through evolution (or in our case, technology). I would definitely not argue that because tardigrades can survive exposure to space that they are from space. But like I was saying, a biogenesis in conditions that are stable and likely more common in exoplanets is encouraging for exobiology. And if nothing else, life’s great adaptability suggests that it tends to stay around once it starts.

Just wanted to say that the response from the “science” community (molecular biologists, biochemists, chemists) has not been good.

Whether or not the popular press hear much about it, what I have been hearing is that essentially no one is happy with how this was published/accepted with the claims included.

It may be exciting that this bacteria can live in high levels of Arsenic (no one seems to doubt/question that), but no one I have spoken with thinks that the Arsenic is actually in the DNA (or even RNA).

And even if it is, the amount present would likely be on order of finding a needle in a small hay stack. You would hardly consider that a “needle stack”.

But one never knows… future work could back up their claims.

It is disappointing. However, peer review, skepticism and analysis is what science is all about! I would rather learn an unromantic fact than a romantic falsehood – unfortunately, psychology doesn’t seem to go in that direction.

400 degrees C might have been a tad exaggerated, but my point was that stability and safety might not be the right conditions for abiogenesis. A crucial role might have been played by something that stirs things up, like radiation, high temperatures, UV light, electrical discharges, noxious chemistry, who knows what. Something not well described by “wet and warm”. Something that would be deadly to today’s complex life, but was necessary to put together the first, much more primitive precursors of life.

One of the inhibiting factors for the early rise of life may have been high levels of UV, particularly UV B, in the young sun. It is known that young solar type stars, during their youth (several hundred million years) emit quite high levels of aggressive UV, a killer for most living cells.

Backlash from the “arsenic life” paper that was published on December 2, is still ongoing. Some of the criticism has been about the science, while much more criticism has been about the coverage of the news and also how NASA introduced, or “teased” the public with news, using the words “astrobiology” and “extraterrestrial life” in their announcement of an upcoming press conference.

Today, at the American Geophysical Union conference, one of the team scientists, Ron Oremland discussed the fallout from the news coverage, and I’ll be providing an overview of that shorty. At about the same time, the science team released a statement and some FAQ’s about the science paper. Below is that statement and the information the science team provided.

Larry, I skimmed the Universe Today article. They sound even more like they don’t know what they’re doing. Example: “Additionally, DNA extracted in this manner on other samples was also successfully used in further analyses, including PCR, that require highly purified DNA.”

PCR does not require purified DNA. In fact, one of its great advantages is that you can do it with dirty DNA or complex DNA mixes. Also, if the polymerase amplified the DNA, it’s further proof that it didn’t contain much arsenic. Finally, had they done these experiments when they submitted the paper, they would have said so, adding “Data not shown.” The paper does not contain such a statement. This borders on disingenuousness.

Charlie Jane Anders and Gordon Jackson — With a possible two billion Earth-like planets in our galaxy alone, the chances of extraterrestrial life are looking better and better. What will these creatures, shaped by another world, look like? It’s up to science fiction creators to imagine them.

But how can you create an alien life form that’s really different than anything you’ll find on Earth, rather than just a slightly tweaked version of a human or other Earth creature? We talked to xenobiologists, and did extensive research, to create a step-by-step guide to creating a truly alien life form from the ground up. Don’t create life without reading this handy guide!

The notion that bacteria can transmit radio waves is controversial. But physicists now say they know how it could be done

kfc 04/25/2011

Can bacteria generate radio waves?

On the face of it, this seems an unlikely proposition. Natural sources of radio waves include lightning, stars and pulsars while artificial sources include radar, mobile phones and computers. This is a diverse list. So it’s hard to see what these things might have in common with bacteria that could be responsible for making radio waves.

But today, Allan Widom at Northeastern University in Boston and a few pals, say they’ve worked out how it could be done.

They point out that many types of bacterial DNA take the form of circular loops. So they’ve modelled the behaviour of free electrons moving around such a small loop, pointing out that, as quantum objects, the electrons can take certain energy levels.

Widom and co calculate that the transition frequencies between these energy levels correspond to radio signals broadcast at 0.5, 1 and 1.5 kilohertz. And they point out that exactly this kind of signal has been measured in E Coli bacteria.

Let’s make one thing clear: this is a controversial area of science. The measurements of bacterial radio waves were published in 2009 by Luc Montagnier, who won the Nobel Prize for medicine in 2008 for the discovery of HIV. However, Montagnier is a controversial figure and it’s fair to say that his claims are not accepted by most mainstream biologists.

However, one of the criticisms of the work was that there is no known mechanism by which bacteria can generate radio waves. That criticism may now no longer hold.

That means Widom and co may be able to kickstart more work in this area. It is well known that bacterial and other types of cells use electromagnetic waves at higher frequencies to communicate as well as to send and store energy. If cells can also generate radio waves, there’s no reason to think they wouldn’t exploit this avenue too.

A controversial arsenic microbe paper, one that NASA touted as offering insight into alien life, came under heavy criticism on Friday. Scanning electron micrograph of strain

CAPTION Image courtesy of Science/AAAS

Released by Science magazine, the eight critiques offer different blasts at a 2010 paper released by the same journal. It described a microbe which the study authors, led by Felisa Wolfe-Simon of the NASA Astrobiology Institute, suggested was able to incorporate poisonous arsenic into its genes.

The release comes outside Science’s regular publishing schedule, and without the usual advance notice that the journal weekly gives to reporters to allow them to run studies by independent experts for comment.

In a statement, the journal explained its decision to release the on-line “technical comment” papers, which will be formally published in June:

Rosie Redfield of the University of British Columbia has steadfastly raised doubts about the headline-grabbing news about arsenic-based life last November. (If neither arsenic life nor Rosie Redfield ring any bells for you, check out my two pieces for Slate, in December and June.)

Redfield then did something exceptional: she set out to replicate the initial findings, getting the original bacteria and seeing whether they can build DNA from arsenic when deprived of phosphorus.

And then she did something quite unique: she started to chronicle her experiences on her blog. It’s a fascinating peek into the lab notebook of a practicing scientist. Today’s post is especially intriguing:

Last year, with much ballyhoo, NASA held a press conference about a team of biologists claiming that they had found microorganisms that could use arsenic instead of phosphorous as a basis for biological processes.

However, it didn’t take too long before the work was under serious attack by other biologists. Some were snarky, others more reserved, but the message was clear: not too many professional biologists felt the arsenic claim held up to scrutiny. In fact, some said the research paper was so shoddy it should never have been published.

This whole event comes to my mind from time to time, and I’ve been meaning to revisit it. I’ll admit I’m a little embarrassed by how I participated in it — I reported it straight, writing up a blog post relaying what I had learned from the press conference and from reading the paper itself. I am not a biologist, so the details of the paper were beyond me. But being a scientist myself I could glean what I needed for a blog post, especially coupled with the comments from the press conference.

It’s been one year since researchers shook up the scientific world by claiming they bred bacteria that used arsenic in place of phosphorus, and the controversy is still simmering: The lead researcher and her critics say they’re taking a closer look at the microbe at the center of the “weird life” claims.

After hitting the highs and the lows of academic acclaim, Felisa Wolfe-Simon has left her original research group and joined up with Lawrence Berkeley National Laboratory in California to continue her research into the bacterium known as GFAJ-1, which gets its name from the acronym for “Give Felisa a Job.” (No joke!)

“There is so much work to do we’re focusing on that and look forward to communicating our efforts in the coming months,” Wolfe-Simon told me in an email this week.

Meanwhile, Wolfe-Simon’s highest-profile critic, University of British Columbia microbiologist Rosie Redfield, took on the task of replicating the GFAJ-1 experiment. “I’m doing this even though I agree with all the other researchers who said this result is almost certainly wrong,” Redfield told me. “Scientifically, it’s really kind of a waste of time to try to replicate this yourself. But there’s always the possibility that you could be wrong. And more than that, there was just a general sense that, you know, somebody should try.”

Using the electrical signals generated by slime mould to make music creates an instrument musicians can ‘play’ by zapping the creature with light

Physarum polycephalum, better known as slime mould, is a single-celled creature that has attracted considerable attention in recent years for its ability to compute in unconventional ways. Various research groups have watched in barely disguised amazement as these single cells have solved mazes, recreated national motorway networks and even anticipated the timing of periodic events.

Now this extraordinary creature has added another skill to its box of tricks–the ability to make music, or at least to create sound in a controlled fashion.

Physarum grows by creating a network of protoplasmic tubes that stretch from one source of food to another. Much of this creature’s computing power comes from its ability to optimise the properties of this network.

Today, Eduardo Miranda at the University of Plymouth in the UK and a couple of pals say they’ve grown a Physarum cell in a petri dish lined with six electrodes, each topped with an oat flake to attract the protoplasmic tubes.

Miranda and co then measured the electrical activity at each electrode every second as the tubes grew across them, a process that took about a week to cover all the electrodes. They then plotted the results against time to compare the activity in different electrodes.

To create a sound, Miranda and co used the signal from each electrode to control the frequency of an audio oscillator. With each electrode controlling a different range of frequencies, they then added the outputs from all the oscillators to create a complex sound that represents the activity of the Physarum.

Of course, this kind of mixing is rather arbitrary but Miranda and co are mainly interested in the sound production method. They say it is possible to control the electrical activity in different parts of the network of tubes by zapping it with light.

In a sense, this allows them to “play” the Physarum like a musical instrument.

“Our own experiments…demonstrated that varying illumination gradients are good means to tune the plasmodium to produce specific oscillatory behaviours,” they say.

They go even further in abstracting this process. “The time it takes to run experiments with Physarum polycephalum can be tedious,” they complain. So instead of growing the slime mould for real, they also simulated the process on computer to speed up the process of music making, the result being a kind of Physarum synthesiser synthesiser.

That’s certainly a bizarre form of music making but Miranda has put it to good use. Earlier this year, he premiered a piece called Die Lebensfreude in Portugal that featured the Physarum electro-acoustics.

If the goal is to push music-making beyond conventional bounds, Miranda and his colleagues must surely have succeeded. Sadly, we’re unable to judge the result since there is no link in the paper or on his website to any of the resulting sound files.

Charter

In Centauri Dreams, Paul Gilster looks at peer-reviewed research on deep space exploration, with an eye toward interstellar possibilities. For the last seven years, this site has coordinated its efforts with the Tau Zero Foundation, and now serves as the Foundation's news forum. In the logo above, the leftmost star is Alpha Centauri, a triple system closer than any other star, and a primary target for early interstellar probes. To its right is Beta Centauri (not a part of the Alpha Centauri system), with Beta, Gamma, Delta and Epsilon Crucis, stars in the Southern Cross, visible at the far right (image: Marco Lorenzi).

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